Pea (Pisum sativum) produces seeds rich in proteins. However, protein content and seed quality can be impacted by environmental factors including drought. Accumulation of seed storage proteins (SSP) during seed filling is a highly regulated process. While proteomics of SSP deposition in pea seeds is well documented, knowledge of the underlying regulatory gene networks, either in control or stress conditions, is lacking. In this study, a RNA-seq based transcriptome analysis of seed development in control and water stress condition was carried out. Developing seeds were collected at six time points, from late embryogenesis to early maturation. RNA-seq was performed on an Illumina Hiseq3000 and reads were mapped on Pisum sativum v1a genome version. A complete RNA-seq workflow analysis including (i) the annotation of new genes using StringTie, (ii) the analysis of unmapped reads (which could represent up to 24% of the total reads in some samples) using RepeatExplorer and Trinity and (iii) the differential expression analysis using Deseq2, will be presented. These data will help us to decipher the transcriptional regulatory network that controls pea seed development, notably during SSP deposition, and how these processes are impacted by drought. This study is funded under the REGULEG ANR Project (ANR-15-CE20-0001-02) coordinated by J. Buitink (INRA, Angers, France)